An enraged father involved in a bitter custody dispute with his girlfriend over their young son beat her to death with a hammer – then set her body on fire and threw it in a Queens trash bin, cops said yesterday.

John Medina, 27, of East 197th Street in The Bronx, was charged with murder, arson, and criminal possession of a weapon. Police said Medina murdered Edna Figueroa, 33, in the bitter dispute over the 2-year-old boy.

Figueroa’s sister Christina Figueroa, 32, said a tearful Medina had stopped by her house after the murder to tell her he had nothing to do with it.

“He was the devil in disguise,” she said. “And now he has my sister’s blood on his hands.

“He may have loved the kid, but my sister didn’t deserve the way he killed her,” she said.

Figueroa – who lived with his alleged victim for 1999 to 2001 – called cops last week after her sister failed to show up for work or to pick up the boy and his 6-year-old half-sister from their baby sitter.

She told The Post last week, after the woman’s body was discovered, that she feared the kids would be the killer’s next target and hid them at a secret location.

Figueroa became alarmed after reading news reports of a gas-station worker who stumbled on a severely burned corpse in a Dumpster in Laurelton.

She went to police and told them she feared the victim was her sister.